The Application of the Acoustic Complexity Indices (ACI) to Ecoacoustic Event Detection and Identification (EEDI) Modeling

In programs of acoustic survey, the amount of data collected and the lack of automatic routines for their classification and interpretation can represent a serious obstacle to achieving quick results. To overcome these obstacles, we are proposing an ecosemiotic model of data mining, ecoacoustic event detection and identification (EEDI), that uses a combination of the acoustic complexity indices (ACIt_f, ACIf_t, and ACIf_te) and automatically extracts the ecoacoustic events of interest from the sound files. These events may be indicators of environmental functioning at the scale of individual vocal species (e.g., behavior, phenology, and dynamics), the acoustic community (e.g., dawn and dusk chorus), the sound marks (e.g., the flag species of a community), or the soundscape (e.g., sonotope types). The EEDI model is represented by three procedural steps: 1) selecting acoustic data according to environmental variables, 2) detecting the events by creating an ecoacoustic event space (EES) produced by plotting ACIf_t and its evenness (ACIf_te), 3) identifying events according to the level of correlation between the acoustic signature (ACIt_f) of the detected events and an ad hoc library of previously identified events. The EEDI procedure can be extensively used in basic and applied research. In particular, EEDI may be used in long-term monitoring programs to assess the effect of climate change on individual vocal species behavior (fishes, frogs, birds, mammals, and arthropods), population, and acoustic community dynamics. The EEDI model can be also used to investigate acoustic human intrusion in natural systems and the effect in urban areas.     

A new European Landscape Classification (LANMAP): A transparent, flexible and user-oriented methodology to distinguish landscapes

We have developed a new hierarchical European Landscape Classification that can be used as a framework for, e.g., indicator reporting and environmental sampling. Landscapes are ecological meaningful units where many processes and components interact. And as such, landscapes themselves have resulted from long-term interactions of natural abiotic, biotic and anthropogenic processes. A good understanding of landscapes is essential for its assessment, protection, management and planning. An internationally consistent approach is therefore obligatory and the production of landscape classifications and associated maps is an important tool in this context. Although intuitive maps are available there are no consistent quantitative maps of European landscapes. In this paper, landscapes are regarded as forming recognizable parts of the earth's surface and as showing a characteristic ordering of elements. The complex nature of the underlying scientific concepts, which sometimes overlap and conflict, requires an objective and consistent methodology, as described in the present paper. As there are many regional differences in landscape properties, it is crucial to strike the right balance between reducing the inherent complexity and maintaining an adequate level of detail. Against this background, a European Landscape Map (LANMAP) has been produced, making use of available segmentation and classification techniques on high-resolution spatial data sets. LANMAP is a landscape classification of Pan-Europe with four hierarchical levels; using digital data on climate, altitude, parent material and land use as determinant factors; and has 350 landscape types at the most detailed level. At this level there are 14,000 mapping units with a minimum mapping unit of 11 km². Thus far, LANMAP is limited to a biophysical approach, since there is a lack of consistent and European-wide data on cultural–historical factors. This paper describes the conceptual background of LANMAP, its methodology and results, and shows its potentials and limitations.     

A new method to measure intestinal activity of P-glycoprotein in avian and mammalian species

Permeability-glycoprotein (Pgp) actively exports numerous potentially toxic compounds once they diffuse into the cell membrane of intestinal epithelial cells. We adapted the everted sleeve technique to make the first measures of intestinal Pgp function in an avian species (chicken) and in wild mammalian species, and compared them to laboratory rats. Tissues maintained both structural and functional integrity, and our method offers advantages over other in vitro techniques by using smaller intestinal sections (1 cm), and shorter incubation times (8–12 min). To determine Pgp function, we compared accumulation of [³H]-digoxin in sleeves incubated in Ringer solution with and without a transport-saturating concentration of a competitive inhibitor, cyclosporin A. We demonstrated significant variation in Pgp activity within individuals along the intestine, between populations fed different diets, and between species (laboratory rats had one-third to one-fifth the Pgp activity of wild rodents). In chicken, we also tested the effect of natural metabolites on digoxin accumulation. We found that among flavonoids, genistein (200 M), found in soy and other legumes, but not quercetin (10, 30, 100, 330 M) or the 3--glycoside isoquercetrin (100 M), significantly increased digoxin accumulation. Among fungal metabolites, sterigmatocystin (5 M), but not aflatoxin B1 (5 M), significantly increased digoxin accumulation.     

Using motion-sensor camera technology to infer seasonal activity and thermal niche of the desert tortoise (Gopherus agassizii)

Understanding the relationships between environmental variables and wildlife activity is an important part of effective management. The desert tortoise (Gopherus agassizii), an imperiled species of arid environments in the southwest US, may have increasingly restricted windows for activity due to current warming trends. In summer 2013, we deployed 48 motion sensor cameras at the entrances of tortoise burrows to investigate the effects of temperature, sex, and day of the year on the activity of desert tortoises. Using generalized estimating equations, we found that the relative probability of activity was associated with temperature (linear and quadratic), sex, and day of the year. Sex effects showed that male tortoises are generally more active than female tortoises. Temperature had a quadratic effect, indicating that tortoise activity was heightened at a range of temperatures. In addition, we found significant support for interactions between sex and day of the year, and sex and temperature as predictors of the probability of activity. Using our models, we were able to estimate air temperatures and times (days and hours) that were associated with maximum activity during the study. Because tortoise activity is constrained by environmental conditions such as temperature, it is increasingly vital to conduct studies on how tortoises vary their activity throughout the Sonoran Desert to better understand the effects of a changing climate.     

The Acclimatization Thermal Strain Index (ATSI): a preliminary study of the methodology applied to climatic conditions of the Russian Far East

Travel to distant places where the climate is different to that at home involves a period of short-term acclimatization adjustment following arrival during which the traveler might experience thermally-induced physiological strain. This may be expressed as an “acclimatization thermal loading” (ATL). The first signs of this show up in the respiratory organs. In the current study, the Acclimatization Thermal Strain Index (ATSI) is developed and used for assessment of ATL for recreational travel over a range of climatic conditions. ATSI estimates the impact of short-term acclimatization calculated as the ratio of a difference between respiratory heat losses at the traveler’s home location to respiratory heat losses at the trip destination upon first arriving there. The Russian Far East region is used as a case study. The research focuses on the effects of travel from two locations in the study region. The results show that ATSI values can be significantly different when considering places of trip origin. For example, travel from Anadyr to other locations within the Russian Far East could lead to large ATSI in summer. In contrast, ATSI values are small for travel almost anywhere in the region during winter, but this is against a backdrop of extreme cold for the region as a whole. Here, the diversity of climatic conditions of both heat and cold means short-term adjustment to conditions could be stressful or worse for those who travel to participate in outdoor activities.     

Spermiogenesis and sperm in Mesostoma viaregginum (Plathelminthes, Rhabdocoela): an ultrastructural study to infer sperm orientation

Spermiogenesis in Mesostoma viaregginum begins with the formation of a zone of differentiation containing striated rootlets, two centrioles, and an intercentriolar body in-between. These centrioles generate two parallel free-flagella with the 9+“1” pattern of the Trepaxonemata growing out in opposite directions. Spermatid differentiation is characterised by a 90° latero-ventral rotation of flagella and a subsequent disto-proximal centriolar rotation, with a distal cytoplasmic projection. The former rotation involves the compression of a row of cortical microtubules and allows recognising a flagellar side and an aflagellar side in the late spermatid and in the mature spermatozoon. At the end of the differentiation, centrioles and microtubules lie parallel to the spermatid axis. The disto-proximal centriolar rotation is proposed as a synapomorphy for the Rhabdocoela. The modifications of the intercentriolar body during spermiogenesis and the migration of the nucleus and the centrioles towards the cytoplasmic distal projection are also described. The mature spermatozoon of M. viaregginum is filiform and tapered at both ends and presents many features found in the Rhabdocoela gametes. The nucleus disappears before the flagellar insertion and a density gradient of mitochondria is observed along the sperm axis. The anterior end of the spermatozoon of M. viaregginum is characterised by a tapering capped by a membrane expansion. This study has enabled us to describe precisely the orientation of spermatozoa in the Rhabdocoela in general: the centriolar extremity is proposed as the anterior one for the Rhabdocoela.     

Motion from the past. A new method to infer vestibular capacities of extinct species

The vestibular system detects head movement in space and maintains visual and postural stability. The semicircular canal system is responsible for registering head rotation. How it responds to head rotation is determined by the rotational axis and the angular acceleration of the head, as well as the sensitivity and orientation of each semicircular canal. The morphological parameters of the semicircular canals are supposed to allow an optimal detection of head rotations induced by some behaviours, especially locomotor. We propose a new method of semicircular canal analysis, based on the computation of central streamlines of virtually reconstructed labyrinths. This method allows us to ascertain the functional structure of the semicircular canal system and to infer its capacity to detect particular head rotations, induced by particular behaviours. In addition, this method is well-suited for datasets provided by any kind of serial sectioning methods, from MRI to μCT scanning and even mechanical serial sectioning, of extant and extinct taxa.     

The refractive development of the eye of the American kestrel (Falco sparverius): a new avian model

Summary Most measures of avian visual performance are carried out on commonly available domestic species such as the chicken, and most of the data on avian induced refractive error deals with chickens. Raptors are predatory birds in which good visual resolving ability is particularly important. Behavioral studies indicate that the eyes of raptors have two to three times the resolving ability of the human eye. The domestic chicken is precocial at hatching whereas most raptors are semi-altricial. This study was an effort to determine if the effect of early visual deprivation on the refractive development of the chicken eye can be reproduced in the American kestrel, a species which is not domesticated and in which the need for acute vision is particularly important.Visual deprivation was achieved by unilaterally applying translucent plastic goggles over the eyes of kestrels two days after hatching. Refractive error was measured using a retinoscope and trial lenses. Ocular growth was monitored by A-scan ultrasonography, and frozen ocular sections of sacrificed birds. The effect of the experimental manipulation on the contralateral control eye and body weight was evaluated each day over a 42-day period. The goggles did not significantly affect the normal changes in body weight or the normal pattern of ocular growth and refractive development in the untreated eyes. An analysis of the refractive state changes as a result of form deprivation was made each week for 6 weeks after hatching on both the treated and untreated eyes in a separate group of experimental birds. Visual form deprivation caused a significant myopic shift in refractive error and a significant increase in the vitreous chamber depth in the treated eyes at 3 and 6 weeks of age. However, the amount of myopia produced is much less than that induced in chicks, and in certain cases hyperopia is produced. The kestrels recover from myopia and hyperopia within 10 days of goggle removal, after 3 to 4 weeks of deprivation.This study is the first indication that chickens may not be a representative bird model for studying form deprivation myopia. First, myopia is not always produced in kestrels in response to form deprivation. Second, kestrels are severely myopic at hatching and therefore, the direction of emmetropization is opposite to that found in hatchling chicks.     

Karyotype of an avian schistosome Trichobilharzia szidati (Digenea: Schistosomatidae)

Somatic chromosomes of Trichobilharzia szidati Neuhaus, 1952 are described from larval stages dissected from snoils, air-dried on slides and stained with Giemsa and C-banding technique, used for the first time in Trichobilharzia sp. The karyotype consisted of 7 autosomal pairs and 1 pair of sex chromosomes, ZZ in the male and ZW in the female, where Z and W chromosomes are of different sizes and both are classified as submetaceatric. C-banding aided in identification of chromosomes Nos 4, satellited 6 and 8. No heterochromatin was observed in the W chromosome. The results were not in agreement with those previously reported and represent new findings. The possible explanation for this fact is given.     

The evolution of rbcL: A methodology to follow the evolution patterns of Medicago and Sulla (Fabaceae) genera

The chloroplast rbcL gene is selected to be a standard barcode for the phylogenetic analyses of several land plants. Using universal primers pair, the 3’ frame was used to assess the phylogeny of the two Legume genera Medicago and Sulla and the evolution of the translated protein. The multiple alignment exhibited high conservation rates (97.56% and 96.43% for Medicago and Sulla respectively), which might be a brake for the phylogenetic assessment. Nevertheless, the topologies of the cladograms drawn using Maximum Likelihood method, showed a low intraspecific divergence and a slightly high interspecific variation, which confirms the efficiency of rbcL for such characterization’ analyses. Besides, the composition and the patterns of the Amino-Acid sequence and the deduced Codon Usage, highlighted a non-aleatoire distribution of the codons. Thus, the non-synonymous substitutions rates traduced a positive selection occurring in the rbcL of the Medicago and Sulla species.     

A new methodology for compiling national Red Lists applied to butterflies (Lepidoptera, Rhopalocera) in Flanders (N-Belgium) and the Netherlands

The compilation of the Red Lists of butterflies in Flanders and the Netherlands was based on two criteria: a trend criterion (degree of decline) and a rarity criterion (actual distribution area). However, due to the large difference in mapping intensity in the two compared periods, a straightforward comparison of the number of grid cells in which each species was recorded, appeared inappropriate. To correct for mapping intensity we used reference species that are homogeneously distributed over the country, that have always been fairly common and that did not fluctuate in abundance too much during this century. For all resident species a relative presence in two compared periods was calculated, using the average number of grid cells in which these reference species were recorded as a correction factor. The use of a standardized method and well-defined quantitative criteria makes national Red Lists more objective and easier to re-evaluate in the future and facilitates the comparison of Red Lists among countries and among different organisms. The technique applied to correct for mapping intensity could be useful to other organisms when there is a large difference in mapping intensity between two periods.     

The haemoproteids (Apicomplexa: Haemoproteidae) of the flowerpeckers of the avian family Dicaeidae (Passeriformes)

The haemoproteids of the flowerpecker family Dicaeidae are reviewed. Two new species, Haemoproteus dicaeus and H. nucleophilus, are described. Haemoproteus nucleophilus appears to be endemic in the dicaeids endemic to the New Guinea archipelago.     

Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae)

The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.     

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.     

Prodepin: A new product of the adrenomedullin (ADM) gene has systemic vasodilator activity

The purpose of the present study was to investigate the effects of products of the ADM gene other than ADM on systemic hemodynamics in the anesthetized rat, rabbit, piglet, cat and dog. Bolus intravenous (i.v.) injections of rat proADM_22–41 (3–30μg) significantly decreased systemic arterial pressure (SAP) and systemic vascular resistance in the anesthetized rat. Unlike ADM, rat proADM_22–41 markedly increased cardiac output in the rat. Bolus i.v. injections of human proADM_22–41 up to 500μm had not effect in all species studied and rat proADM_22–41 had no effect in species other than the rat. The present data suggest that rat proADM_22–41 is a novel product of the ADM gene other than ADM and possesses marked systemic vasodilator activity. The present data also suggest that the hemodynamic activity of this peptide is species specific.     

Establishment of exotic parasites: the origins and characteristics of an avian malaria community in an isolated island avifauna

Knowledge of the processes favouring the establishment of exotic parasites is poor. Herein, we test the characteristics of successful exotic parasites that have co-established in the remote island archipelago of New Zealand, due to the introduction of numerous avian host species. Our results show that avian malaria parasites (AM; parasites of the genus Plasmodium) that successfully invaded are more globally generalist (both geographically widespread and with a broad taxonomic range of hosts) than AM parasites not co-introduced to New Zealand. Furthermore, the successful AM parasites are presently more prevalent in their native range than AM parasites found in the same native range but not co-introduced to New Zealand. This has resulted in an increased number and greater taxonomic diversity of AM parasites now in New Zealand.